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A map of intra- and intercellular immune responses across diverse in vitro stimuli and inflammatory disease
Oliver Wood1, Adam T Braithwaite1, Josephine Fisher1
1Gilead Sciences, 9400 Oxford Business Park, Garsington, Oxford, OX4 2HN, UK.
Insights
This study maps human immune cell responses to 11 common in vitro stimuli using single-cell transcriptomics. It reveals stimulus-specific immune signatures and models aspects of inflammatory diseases like SLE, highlighting limitations of in vitro systems.
Area of Science:
- Immunology
- Systems Biology
- Transcriptomics
Background:
- In vitro stimulation of human immune cells is crucial for disease modeling and therapeutic testing.
- Current research often lacks comprehensive cellular comparisons of immunomodulators and their disease relevance.
Purpose of the Study:
- To create a reference profile of human peripheral blood mononuclear cells (PBMCs) responding to 11 distinct in vitro stimuli.
- To enable comparative analyses of immunomodulatory effects across cell types and in relation to inflammatory diseases.
Main Methods:
- Utilized single-cell transcriptomics on over 150,000 cells from 21 immune cell types.
- Treated PBMCs with 11 different in vitro stimuli.
- Performed comparative analyses against patient-derived inflammatory disease datasets.
Main Results:
- Characterized transcriptomic responses unique to and shared across stimuli, with some stimuli (e.g., anti-CD3, IFN-α) inducing broad activation and others (e.g., TNF-α, LPS) showing cell-specific effects.
- Identified dominant intercellular signaling pathways via ligand-receptor interaction mapping.
- Demonstrated that certain stimuli recapitulate aspects of inflammatory diseases (e.g., IFN-α for SLE, LPS for monocytes) but noted limitations in modeling complex intercellular interactions.
Conclusions:
- The generated dataset serves as a valuable resource for understanding in vitro immune cell stimulation.
- Provides cellular-resolution insights into the similarities and differences of common stimuli.
- Guides the appropriate application of in vitro systems for modeling human diseases.
Background:
In vitro stimulation of healthy human immune cells is widely used to model the immune states observed in disease, both to investigate pathology and to test therapeutic approaches. However, experiments typically focus on individual cell types or stimuli and a comprehensive cellular comparison of common immunomodulators and their relevance to disease is lacking.
Methods:
We used single-cell transcriptomics to generate a reference profile of human peripheral blood mononuclear cells treated with 11 different in vitro stimuli, totalling over 150,000 cells across 21 immune cell types. We demonstrate its utility by performing comparative analyses across the immunomodulatory conditions and against peripheral blood profiles from patients with inflammatory disease.
Results:
We describe transcriptomic responses both unique to and shared across stimuli. For instance, stimulation via the T cell receptor (anti-CD3, CytoStim™) and IFN-α induced broad activation signatures, including indirect effects across multiple cell types, whereas TNF-α and LPS elicited more restricted, cell-specific responses. Ligand-receptor interaction mapping also uncovered the dominant intercellular signalling pathways in each stimulation. Comparing to patient datasets, we identified several aspects of inflammatory disease recapitulated by stimuli. For example, IFN-α stimulation induced SLE-like signatures across cell types, whereas LPS did so specifically within monocytes. However, comparative cell-cell network analysis showed that in vitro stimuli were only able to recapitulate some, but not all, aspects of intercellular interactions upregulated in SLE, highlighting the limitations of these model systems.
Conclusions:
This dataset provides a valuable resource for understanding the effects of common in vitro blood stimuli, offering insights into their similarities and differences at cellular resolution, and, as demonstrated here, helping to guide the appropriate use of in vitro systems to model disease.
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